Region Based Structure Layout Optimization by Selective Data Copying

As the gap between processor and memory continues to grow Memory performance becomes a key performance bottleneck for many applications. Compilers therefore increasingly seek to modify an application’s data layout to improve cache locality and cache reuse. Whole program Structure Layout [WPSL] transformations can significantly increase the spatial locality of data and reduce the runtime of programs that use link-based data structures, by increasing the cache line utilization. However, in production compilers WPSL transformations do not realize the entire performance potential possible due to a number of factors. Structure layout decisions made on the basis of whole program aggregated affinity/hotness of structure fields, can be sub optimal for local code regions. WPSL is also restricted in applicability in production compilers for type unsafe languages like C/C++ due to the extensive legality checks and field sensitive pointer analysis required over the entire application. In order to overcome the issues associated with WPSL, we propose Region Based Structure Layout (RBSL) optimization framework, using selective data copying. We describe our RBSL framework, implemented in the production compiler for C/C++ on HP-UX IA-64. We show that acting in complement to the existing and mature WPSL transformation framework in our compiler, RBSL improves application performance in pointer intensive SPEC benchmarks ranging from 3% to 28% over WPSL

Use of structure-directed DNA ligands to probe the binding of recA protein to narrow and wide grooves of DNA and on its ability to promote homologous pairing

We have used circular dichroism and structure-directed drugs to identify the role of structural features, wide and narrow grooves in particular, required for the cooperative polymerization, recognition of homologous sequences, and the formation of joint molecules promoted by recA protein. The path of cooperative polymerization of recA protein was deduced by its ability to cause quantitative displacement of distamycin from the narrow groove of duplex DNA. By contrast, methyl green bound to the wide groove was retained by the nucleoprotein filaments comprised of recA protein-DNA. Further, the mode of binding of these ligands and recA protein to DNA was confirmed by DNaseI digestion. More importantly, the formation of joint molecules was prevented by distamycin in the narrow groove while methyl green in the wide groove had no adverse effect. Intriguingly, distamycin interfered with the production of coaggregates between nucleoprotein filaments of recA protein-M13 ssDNA and naked linear M13 duplex DNA, but not with linear phi X174 duplex DNA. Thus, these data, in conjunction with molecular modeling, suggest that the narrow grooves of duplex DNA provide the fundamental framework required for the cooperative polymerization of recA protein and alignment of homologous sequences. These findings and their significance are discussed in relation to models of homologous pairing between two intertwined DNA molecules.

Nanoscale compositional analysis of NiTi shape memory alloy films deposited by DC magnetron sputtering

The formation of surface oxide layer as well as compositional changes along the thickness for NiTi shape memory alloy thin films deposited by direct current magnetron sputtering at substrate temperature of 300 degrees C in the as-deposited condition as well as in the postannealed (at 600 degrees C) condition have been thoroughly studied by using secondary ion mass spectroscopy, x-ray photoelectron spectroscopy, and scanning transmission electron microscopy-energy dispersive x-ray spectroscopy techniques. Formation of titanium oxide (predominantly titanium dioxide) layer was observed in both as-deposited and postannealed NiTi films, although the oxide layer was much thinner (8 nm) in as-deposited condition. The depletion of Ti and enrichment of Ni below the oxide layer in postannealed films also resulted in the formation of a graded microstructure consisting of titanium oxide, Ni3Ti, and B2 NiTi. A uniform composition of B2 NiTi was obtained in the postannealed film only below a depth of 200-250 nm from the surface. Postannealed film also exhibited formation of a ternary silicide (NixTiySi) at the film-substrate interface, whereas no silicide was seen in the as-deposited film. The formation of silicide also caused a depletion of Ni in the film in a region similar to 250-300 nm just above the film substrate interface. (C) 2013 American Vacuum Society.

Graphical method to include temperature variation of activation energy in Hall data analysis

A graphical method is presented for Hall data analysis, including the temperature variation of activation energy due to screening. This method removes the discrepancies noted in the analysis of recently reported Hall data on Si(In).

Epidemiology of symptomatic human rotaviruses in Bangalore and Mysore, India, from 1988 to 1994 as determined by electropherotype, subgroup and serotype analysis

Epidemiology of symptomatic rotaviruses from Bangalore and Mysore in Southern India was investigated. While serotype G3 predominated throughout the 7-year study period from 1988 to 1994 in Bangalore, serotype G1 was more predominant than serotype G3 in Mysore during 1993 and 1994. Serotype G2 strains were either not detected or infrequently observed in both the cities. However, several strains with subgroup I and lsquoshortrsquo RNA pattern that exhibited high reactivity with typing MAbs specific for serotype 2 as well as other serotypes were detected throughout the period. Among the nonserotypeable strains from both cities, several exhibited dual subgroup (SGI+II) or subgroup I specificity and lsquolongrsquo RNA pattern indicating their probable animal origin. Notably, a gradual, yet highly significant reduction in rotavirus gastroenteritis, from 45.3% in 1988 to 1.8% during 1994, was observed in Bangalore in stark contrast to the consistently high (about 34%) incidence of asymptomatic infections among neonates by I321-like G10P11 type strains during the same period. Moreover, I321-like asymptomatic strains were not detected in children with diarrhea.

Discovering user preferences by using time entries in click-through data to improve search engine results

The search engine log files have been used to gather direct user feedback on the relevancy of the documents presented in the results page. Typically the relative position of the clicks gathered from the log files is used a proxy for the direct user feedback. In this paper we identify reasons for the incompleteness of the relative position of clicks for deciphering the user preferences. Hence, we propose the use of time spent by the user in reading through the document as indicative of user preference for a document with respect to a query. Also, we identify the issues involved in using the time measure and propose means to address them.

Data compression by linear prediction for storage and transmission of EEG signals

The EEG time series has been subjected to various formalisms of analysis to extract meaningful information regarding the underlying neural events. In this paper the linear prediction (LP) method has been used for analysis and presentation of spectral array data for the better visualisation of background EEG activity. It has also been used for signal generation, efficient data storage and transmission of EEG. The LP method is compared with the standard Fourier method of compressed spectral array (CSA) of the multichannel EEG data. The autocorrelation autoregressive (AR) technique is used for obtaining the LP coefficients with a model order of 15. While the Fourier method reduces the data only by half, the LP method just requires the storage of signal variance and LP coefficients. The signal generated using white Gaussian noise as the input to the LP filter has a high correlation coefficient of 0.97 with that of original signal, thus making LP as a useful tool for storage and transmission of EEG. The biological significance of Fourier method and the LP method in respect to the microstructure of neuronal events in the generation of EEG is discussed.

Application of principal component analysis to gas sensing characteristics of Cr0.8Fe0.2NbO4 thick film array

The transient changes in resistances of Cr0.8Fe0.2NbO4 thick film sensors towards specified concentrations of H-2, NH3, acetonitrile, acetone, alcohol, cyclohexane and petroleum gas at different operating temperatures were recorded. The analyte-specific characteristics such as slopes of the response and retrace curves, area under the curve and sensitivity deduced from the transient curve of the respective analyte gas have been used to construct a data matrix. Principal component analysis (PCA) was applied to this data and the score plot was obtained. Distinguishing one reducing gas from the other is demonstrated based on this approach, which otherwise is not possible by measuring relative changes in conductivity. This methodology is extended for three Cr0.8Fe0.2NbO4 thick film sensor array operated at different temperatures. (C) 2015 Elsevier B.V. All rights reserved.

Specific immunoneutralization of FSH leads to apoptotic cell death of the pachytene spermatocytes and spermatogonial cells in the rat

Although requirement for follicle stimulating hormone (FSH) in the initiation of spermatogenesis is well documented, its role in adult spermatogenesis is still debated. In the present communication, we have investigated the effect of specific immunoneutralization of FSH on apoptotic cell death in the testicular germ cells both in immature and adult rats. The germ cells of control animals showed predominantly high molecular weight DNA while the antiserum (a/s) treated group showed DNA fragmentation characteristic of apoptosis. The pattern could be detected within 24 hours of a/s treatment, and became more pronounced after 48 hours. The germ cells were purified from FSH a/s treated rats by centrifugal elutriation and vulnerability of each cell type to undergo apoptosis on FSH neutralization was investigated. The pachytene spermatocytes were found to be most sensitive to absence of FSH, even in the adult animals suggesting the involvement of FSH in spermatogenesis. The in situ analysis of DNA strand breakage following FSH a/s treatment showed fragmentation of the DNA of the pachytene spermatocytes confirming this observation. The in situ analysis also showed that the spermatogonia undergo apoptosis in addition to the pachytene spermatocytes. These data clearly demonstrate the role of FSH in the adult rat spermatogenesis.

X-ray Crystallographic Analysis of the Complexes of Enoyl Acyl Carrier Protein Reductase of Plasmodium falciparum with Triclosan Variants to Elucidate the Importance of Different Functional Groups in Enzyme Inhibition

Triclosan, a well-known inhibitor of Enoyl Acyl Carrier Protein Reductase (ENR) from several pathogenic organisms, is a promising lead compound to design effective drugs. We have solved the X-ray crystal structures of Plasmodium falciparum ENR in complex with triclosan variants having different substituted and unsubstituted groups at different key functional locations. The structures revealed that 4 and 2' substituted compounds have more interactions with the protein, cofactor, and solvents when compared with triclosan. New water molecules were found to interact with some of these inhibitors. Substitution at the 2' position of triclosan caused the relocation of a conserved water molecule, leading to an additional hydrogen bond with the inhibitor. This observation can help in conserved water-based inhibitor design. 2' and 4' unsubstituted compounds showed a movement away from the hydrophobic pocket to compensate for the interactions made by the halogen groups of triclosan. This compound also makes additional interactions with the protein and cofactor which compensate for the lost interactions due to the unsubstitution at 2' and 4'. In cell culture, this inhibitor shows less potency, which indicates that the chlorines at 2' and 4' positions increase the ability of the inhibitor to cross multilayered membranes. This knowledge helps us to modify the different functional groups of triclosan to get more potent inhibitors. (C) 2010 IUBMB IUBMB Life, 62(6): 467-476.

Preparation and characterization of rubidium-beta-alumina by the gel-to-crystallite conversion method

Preparation of Rb-beta -alumina was realized by the gel-to-crystallite conversion method. Reaction of hydrated aluminum hydroxide gel with RbOH in ethanol medium gave rise to the Rb+-inserted pseudoboehmite precursor under wet chemical conditions. The thermal decomposition of the precursor yielded Rb-beta -alumina. The Rb2O:Al2O3 ratio of monophasic Rb-beta -alumina ranged from 1:10 to 1:22. The extended stability in the compositional range is due to the fact that the conduction planes containing Rb+ and O2- ions can have lower occupancy of Rb+ ions for larger sized alkali ions, permitting the steric separation of the adjoining spinel blocks. High-resolution electron microscopy revealed that the decreasing occupancy of alkali ions in the conduction plane is balanced by changing widths of spinel blocks arising from the shift of tetrahedral Al3+ ions to octahedral sites and an accompanying increase in stacking defects. (C) 2000 Elsevier Science Ltd. All rights reserved.

Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of α-conotoxin GI and edothelin I

A general procedure for arriving at 3-D models of disulphiderich olypeptide systems based on the covalent cross-link constraints has been developed. The procedure, which has been coded as a computer program, RANMOD, assigns a large number of random, permitted backbone conformations to the polypeptide and identifies stereochemically acceptable structures as plausible models based on strainless disulphide bridge modelling. Disulphide bond modelling is performed using the procedure MODIP developed earlier, in connection with the choice of suitable sites where disulphide bonds could be engineered in proteins (Sowdhamini,R., Srinivasan,N., Shoichet,B., Santi,D.V., Ramakrishnan,C. and Balaram,P. (1989) Protein Engng, 3, 95-103). The method RANMOD has been tested on small disulphide loops and the structures compared against preferred backbone conformations derived from an analysis of putative disulphide subdatabase and model calculations. RANMOD has been applied to disulphiderich peptides and found to give rise to several stereochemically acceptable structures. The results obtained on the modelling of two test cases, a-conotoxin GI and endothelin I, are presented. Available NMR data suggest that such small systems exhibit conformational heterogeneity in solution. Hence, this approach for obtaining several distinct models is particularly attractive for the study of conformational excursions.

Multifractal analysis, a method to investigate the morphology of materials

Using the multifractal formalism, we discuss the results obtained to characterized the morphology of polymer alloys and granular discontinuous metallic thin films. In the first case we have found a correlation between the multifractality and the mechanical properties of the alloys. In the second case, we have found that it is possible to measure the differences between the morphology of thin films induced by a growth process on a subtrate and that of percolation clusters of the classical theory of percolation.

Synthesis, crystal structure and catalytic properties of (p-cymene)ruthenium(II) azophenol complexes: azophenyl to azophenol conversion by oxygen insertion to a ruthenium---carbon bond

Azophenol complexes of formulation [(η6-p-cymene)RuCl(Ln)] (1–6, n=1–6) were prepared by two synthetic methods involving either an oxygen insertion to the Ru---C bond in cycloruthenated precursors forming complexes 1 and 2 or from the reaction of [{(η6-p-cymene)RuCl}2(μ-Cl)2] with azophenol ligands (HL3–HL6) in the presence of sodium carbonate in CH2Cl2. The molecular structure of the 1-(phenylazo)-2-naphthol complex has been determined by X-ray crystallography. The complex has a η6-p-cymene group, a chloride and a bidentate N,O-donor azophenol ligand. The complexes have been characterized from NMR spectral data. The catalytic activity of the complexes has been studied for the conversion of acetophenone to the corresponding alcohol in the presence of KOH and isopropanol. Complexes 4 and 6 having a methoxy group attached to the ortho-position of the phenylazo moiety and 2 with a methyl group in the meta-position of the phenolic moiety show high percentage conversion (>84%).